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Singh-Lab/FBApro

Authors: Ariel Bruner and Mona Singh


Abstract

Cite as

Ariel Bruner, Mona Singh. Singh-Lab/FBApro (Software, Source Code). Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)


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@misc{dagstuhl-artifact-27640,
   title = {{Singh-Lab/FBApro}}, 
   author = {Bruner, Ariel and Singh, Mona},
   note = {Software, swhId: \href{https://archive.softwareheritage.org/swh:1:dir:56f800231d0dae5268df2adbab6fd5599d0a376f;origin=https://github.com/Singh-Lab/FBApro;visit=swh:1:snp:6a6af8056f089d37136c49d4b7ed3a5bb8f4d1e0;anchor=swh:1:rev:ce7cab975f68796659f9e52581320d5cb3093a2d}{\texttt{swh:1:dir:56f800231d0dae5268df2adbab6fd5599d0a376f}} (visited on 2026-08-27)},
   url = {https://github.com/Singh-Lab/FBApro},
   doi = {10.4230/artifacts.27640},
}
Document
FBApro: A Fast, Simple Linear Transformation for Diverse Metabolic Modeling Tasks

Authors: Ariel Bruner and Mona Singh

Published in: LIPIcs, Volume 390, 26th International Conference on Algorithms for Bioinformatics (WABI 2026)


Abstract
Constraint-based metabolic modeling is the predominant framework for simulating cellular metabolism. The central assumption of these models is that metabolism operates at a steady state, meaning that the production and consumption rates of each metabolite are balanced. This assumption imposes linear constraints on the fluxes of biochemical reactions. Flux Balance Analysis (FBA), a fundamental method in the field, is formulated as an optimization problem maximizing a cellular objective (e.g., growth) over the resulting linear subspace of steady state fluxes. Many other methods in the field are expressed either as a modification to FBA, or use FBA as a black box within an algorithm. Here, we propose a general alternative to optimization called FBApro. For any given vector of reference fluxes, FBApro finds the closest flux vector within the steady-state subspace, and accounts for both partially given reference fluxes and exact constraints on reactions. While FBApro is the solution to a quadratic program, we show that it can be implemented as a single linear operation using orthogonal projections to corresponding affine spaces and sets of linear equations. The overall approach is computationally efficient, does not require a cellular objective, and is easy to implement. We formally derive the closed-form expressions for FBApro and simpler variants, and validate it on both synthetic and real cancer cell line data. Code availability. The code implementing FBApro is available at https://github.com/Singh-Lab/FBApro. All code required to reproduce the figures in the paper is available, although the data used must be sourced separately. The repository also contains toy models and examples.

Cite as

Ariel Bruner and Mona Singh. FBApro: A Fast, Simple Linear Transformation for Diverse Metabolic Modeling Tasks. In 26th International Conference on Algorithms for Bioinformatics (WABI 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 390, pp. 26:1-26:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)


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@InProceedings{bruner_et_al:LIPIcs.WABI.2026.26,
  author =	{Bruner, Ariel and Singh, Mona},
  title =	{{FBApro: A Fast, Simple Linear Transformation for Diverse Metabolic Modeling Tasks}},
  booktitle =	{26th International Conference on Algorithms for Bioinformatics (WABI 2026)},
  pages =	{26:1--26:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-446-8},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{390},
  editor =	{El-Mabrouk, Nadia and Vandin, Fabio},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2026.26},
  URN =		{urn:nbn:de:0030-drops-275305},
  doi =		{10.4230/LIPIcs.WABI.2026.26},
  annote =	{Keywords: metabolic modeling, flux balance analysis, constraint-based metabolic modeling}
}

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